Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

Conflicts:
	src/jalview/gui/PopupMenu.java
	src/jalview/jbgui/GAlignFrame.java

diff --cc src/jalview/appletgui/APopupMenu.java
Simple merge

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/bin/JalviewLite.java
Simple merge

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/PCAPanel.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
index f3927df,e36204c..ac2fbc2
--- 1/src/jalview/gui/PopupMenu.java
--- 2/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -38,9 -38,8 +38,9 @@@ import jalview.datamodel.Sequence
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceGroup;
  import jalview.datamodel.SequenceI;
 +import jalview.gui.ColourMenuHelper.ColourChangeListener;
- import jalview.io.FileFormat;
  import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
  import jalview.io.FormatAdapter;
  import jalview.io.SequenceAnnotationReport;
  import jalview.schemes.AnnotationColourGradient;
@@@ -199,7 -238,23 +199,7 @@@ public class PopupMenu extends JPopupMe
      this.ap = ap;
      sequence = seq;
  
-     for (String ff : FileFormat.getWritableFormats(true))
 -    ButtonGroup colours = new ButtonGroup();
 -    colours.add(noColourmenuItem);
 -    colours.add(clustalColour);
 -    colours.add(zappoColour);
 -    colours.add(taylorColour);
 -    colours.add(hydrophobicityColour);
 -    colours.add(helixColour);
 -    colours.add(strandColour);
 -    colours.add(turnColour);
 -    colours.add(buriedColour);
 -    colours.add(userDefinedColour);
 -    colours.add(PIDColour);
 -    colours.add(BLOSUM62Colour);
 -    colours.add(purinePyrimidineColour);
 -    colours.add(RNAInteractionColour);
 -
+     for (String ff : FileFormats.getInstance().getWritableFormats(true))
      {
        JMenuItem item = new JMenuItem(ff);
  
@@@ -1829,7 -2279,8 +1829,7 @@@
      // or we simply trust the user wants
      // wysiwig behaviour
  
-     FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
 -    FileFormatI fileFormat = FileFormats.getInstance().forName(
 -            e.getActionCommand());
++    FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
      cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
    }
  

diff --cc src/jalview/gui/Preferences.java
Simple merge

diff --cc src/jalview/jbgui/GAlignFrame.java
index dff20d3,dc17397..a320a9c
--- 1/src/jalview/jbgui/GAlignFrame.java
--- 2/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@@ -23,11 -23,12 +23,11 @@@ package jalview.jbgui
  import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  import jalview.api.SplitContainerI;
  import jalview.bin.Cache;
 -import jalview.gui.JvOptionPane;
  import jalview.gui.JvSwingUtils;
  import jalview.gui.Preferences;
- import jalview.io.FileFormat;
+ import jalview.io.FileFormats;
 -import jalview.schemes.ColourSchemeProperty;
  import jalview.util.MessageManager;
 +import jalview.util.Platform;
  
  import java.awt.BorderLayout;
  import java.awt.Color;